{"name":"workshop-demo","display_name":"workshop demo","visibility":"public","icon":"","categories":[],"schema_version":"0.2.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"workshop-demo.get_reader","title":"tracking challenge reader","python_name":"workshop_demo._reader:napari_get_reader","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"workshop-demo.get_segment_widget","title":"open threshold widget","python_name":"workshop_demo._dock_widget:segment_by_threshold","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"workshop-demo.get_highlight_widget","title":"open highlight widget","python_name":"workshop_demo._dock_widget:SegmentationDiffHighlight","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"workshop-demo.write_labels","title":"save to zip","python_name":"workshop_demo._writer:labels_to_zip","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"workshop-demo.get_reader","filename_patterns":[],"accepts_directories":true}],"writers":[{"command":"workshop-demo.write_labels","layer_types":["labels*"],"filename_extensions":[".zip"],"display_name":"label zipper"}],"widgets":[{"command":"workshop-demo.get_segment_widget","display_name":"Segment by Thresholding","autogenerate":false},{"command":"workshop-demo.get_highlight_widget","display_name":"Highlight Segmentation Differences","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"workshop-demo","version":"0.0.2","dynamic":null,"platform":["UNKNOWN"],"supported_platform":null,"summary":"A demo napari plugin incorporating reader, writer and dock widget contributions using the new npe2 plugin architecture.","description":"# workshop-demo\n\n[![License](https://img.shields.io/pypi/l/workshop-demo.svg?color=green)](https://github.com/DragaDoncila/workshop-demo/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/workshop-demo.svg?color=green)](https://pypi.org/project/workshop-demo)\n[![Python Version](https://img.shields.io/pypi/pyversions/workshop-demo.svg?color=green)](https://python.org)\n[![tests](https://github.com/DragaDoncila/workshop-demo/workflows/tests/badge.svg)](https://github.com/DragaDoncila/workshop-demo/actions)\n[![codecov](https://codecov.io/gh/DragaDoncila/workshop-demo/branch/main/graph/badge.svg)](https://codecov.io/gh/DragaDoncila/workshop-demo)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/workshop-demo)](https://napari-hub.org/plugins/workshop-demo)\n\nA demo napari plugin incorporating reader, writer and dock widget contributions using the new npe2 plugin architecture.\n\n----------------------------------\n\nThis [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.\n\n<!--\nDon't miss the full getting started guide to set up your new package:\nhttps://github.com/napari/cookiecutter-napari-plugin#getting-started\n\nand review the napari docs for plugin developers:\nhttps://napari.org/docs/plugins/index.html\n-->\n\n## Installation\n\nYou can install `workshop-demo` via [pip]:\n\n    pip install workshop-demo\n\n\nTo install latest development version :\n\n    pip install git+https://github.com/DragaDoncila/workshop-demo.git\n\n## What is this?\n\nThis plugin was created to serve as a semi-meaningful example of a plugin using\nthe new napari [npe2](https://pypi.org/project/npe2/) architecture.\n\nIt provides a reader, a writer and two dock widgets to support opening, processing\nand writing out [cell tracking challenge](https://celltrackingchallenge.net/) data.\n\nWe've provided comments and example tests that can be used as a reference\nwhen building your own plugin.\n\n## Using this plugin\n\n### Sample Data\nYou can download sample data for this plugin from the tracking challenge website. Any 2D+T\nsequence should work, but this plugin has been tested only with the \n[Human hepatocarcinoma-derived cells expressing the fusion protein YFP-TIA-1](http://data.celltrackingchallenge.net/training-datasets/Fluo-C2DL-Huh7.zip) \ndataset.\n### Reading Data\nThis plugin's reader is designed for tracking challenge segmentation gold standard ground truth\ndata conforming to the file format described in the [data specification](https://public.celltrackingchallenge.net/documents/Naming%20and%20file%20content%20conventions.pdf).\n\nGround truth data is only provided for a subset of the frames of the entire sequence. This\nreader will attempt to find the number of frames of the associated sequence in a sister\ndirectory of the ground truth data directory and open a labels layer with the same number\nof frames, thus ensuring the labelled data is correctly overlaid onto the original sequence.\n\n\n\nhttps://user-images.githubusercontent.com/17995243/146114062-36124c05-f44a-488e-8991-f39a702c917f.mov\n\n\n\n### Segmenting Data\nOne of the dock widgets provided by this plugin is \"Segment by Threshold\". The widget\nallows you to select a 2D+T image layer in the viewer (e.g. any of the sequences in the Human \nhepatocarcinoma dataset above) and segment it using a selection of scikit-image thresholding functions.\n\nThe segmentation is then returned as a `Labels` layer into the viewer.\n\n\nhttps://user-images.githubusercontent.com/17995243/146114088-f6fb645e-8d78-4880-827b-2f0334dad859.mov\n\n\n\n### Highlighting Segmentation Differences\nThe second dock widget provided by this plugin allows you to visually compare your segmentation\nagainst the ground truth data by computing the difference between the two and adding this as a\nlayer in the napari viewer.\n\nTo use this widget, open it from the Plugins menu and select the two layers you wish to compare.\n\n\n\nhttps://user-images.githubusercontent.com/17995243/146114112-c891723f-8640-4708-8014-c78731fb3396.mov\n\n\n\n### Writing to Zip\nFinally, you can save your segmentation to a zip file whose internal directory structure\nwill closely mimic that of the tracking challenge datasets, so that it may be opened \nagain in the viewer.\n\nTo save your layer, choose File -> Save selected layer(s) with *one* labels layer selected,\nthen select label zipper from the dropdown choices.\n\n\n\nhttps://user-images.githubusercontent.com/17995243/146114163-ee886990-979c-4756-97c5-aaf2c39dccde.mov\n\n\n\n## Contributing\n\nContributions are very welcome. Tests can be run with [tox], please ensure\nthe coverage at least stays the same before you submit a pull request.\n\n## License\n\nDistributed under the terms of the [BSD-3] license,\n\"workshop-demo\" is free and open source software\n\n## Issues\n\nIf you encounter any problems, please [file an issue] along with a detailed description.\n\n[napari]: https://github.com/napari/napari\n[Cookiecutter]: https://github.com/audreyr/cookiecutter\n[@napari]: https://github.com/napari\n[MIT]: http://opensource.org/licenses/MIT\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\n[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt\n[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt\n[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0\n[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt\n[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin\n\n[file an issue]: https://github.com/DragaDoncila/workshop-demo/issues\n\n[napari]: https://github.com/napari/napari\n[tox]: https://tox.readthedocs.io/en/latest/\n[pip]: https://pypi.org/project/pip/\n[PyPI]: https://pypi.org/\n\n\n","description_content_type":"text/markdown","keywords":null,"home_page":"https://github.com/DragaDoncila/workshop-demo","download_url":null,"author":"Draga Doncila Pop","author_email":"ddoncilapop@contractor.chanzuckerberg.com","maintainer":null,"maintainer_email":null,"license":"BSD-3-Clause","classifier":["Development Status :: 2 - Pre-Alpha","Framework :: napari","Intended Audience :: Developers","License :: OSI Approved :: BSD License","Operating System :: MacOS :: MacOS X","Operating System :: POSIX :: Linux","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3 :: Only","Programming Language :: Python :: 3.7","Programming Language :: Python :: 3.8","Programming Language :: Python :: 3.9","Programming Language :: Python :: 3.10","Topic :: Software Development :: Testing"],"requires_dist":["dask[array]","imagecodecs","napari","napari-plugin-engine (>=0.1.4)","npe2","numpy","scikit-image","tifffile"],"requires_python":">=3.7","requires_external":null,"project_url":["Bug Tracker, https://github.com/DragaDoncila/workshop-demo/issues","Documentation, https://github.com/DragaDoncila/workshop-demo#README.md","Source Code, https://github.com/DragaDoncila/workshop-demo","User Support, https://github.com/DragaDoncila/workshop-demo/issues"],"provides_extra":null,"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}